Subsections

2.4 Refinement Dictionaries

Refinement dictionaries are a list of geometrical constraints used by various refinement packages that supply various refinement packages with chemical bonding and molecular conformation information. The quality of the post refinement ligand conformations are directly related to the quality of the constraints[2].

Flynn comes bundled with a refinement dictionary writer suitable named writedict. writedict uses the MMFF94 forcefield to derive geometrical constraints for the input ligands or ligand-protein complexes. The output dictionaries enforce, as closely as possible, the input ligand's geometries while allowing the refinement programs to modify the geometry as needed.

writedict also automatically detects covelent bonds in pdb files and inserts the appropriate PDB LINK records and covalent bond entries in the output refinement dictionary.

2.4.1 Note about REFMAC5 refinement dictionaries

When outputing refmac5 refinement dictionaries, writedict writes out a ``.cif'' file and a ``.pdb'' file. The ``.pdb'' file is written out for two reasons:

Inconsistent Hydrogen Naming - Some applications write out hydrogen names incorrectly in ways that cause refmac5 or visualization programs like coot or WinCoot to not be able to associate the hydrogens in the refinement dictionary with hydrogens in the pdb file. In the worst case, refmac5 will crash entirely.
When necessary, writedict renames and renumbers hydrogens if they exist so that refmac5 won't crash and so the ``.cif'' file is consistent with the ``.pdb'' file.
Covalent Bonds - writedict detects covalent bonds and outputs proper LINK records in the ``.pdb'' file and proper covalent constraints in the ``.cif'' file. Without using both outputs, refmac5 will not detect covalent bonds during refinement.

It is highly recommended to use writedict's generated ``.pdb'' file in conjunction with the ``.cif''.

2.4.2 Note on the MMFF94 versus MMFF94s forcefields

The MMFF94s forcefield is a variant of MMFF94 that emulates time-averaged structures typically observed during crystallographic structure determination, mainly planar geometries at unstrained delocalized trigonal nitrogen centers. However, there are many theoretical studies that show nitrogen centers are puckered[20].

That being said, due to the prevalence of crystallographic examples where time averaging has occured, many chemist erroneously consider the time-averaged structure to be correct, hence this variant is available for use.

writedict approximates the MMFF94s forcefield by enforcing planar aniline nitrogen configurations using the out of plane atom types and parameters from the MMFF94s. See the -planarAniline parameter to specify planar constraints.

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